cgNA+web : A Visual Interface to the cgNA+ Sequence-dependent Statistical Mechanics Model of Double-stranded Nucleic Acids.

The sequence-dependent statistical mechanics of double-stranded nucleic acid, or dsNA, is believed to be essential in its biological functions. In turn, the equilibrium statistical mechanics behaviour of dsNA depends strongly both on sequence-dependent perturbations in its ground state shape away from an idealised, uniform, double-helical configuration, and on its fluctuations as governed by its sequence-dependent stiffness. We here describe the cgNA+web browser-based interactive tool for visualising the sequence-dependent ground states of dsNA fragments of arbitrary sequences, as predicted by the underlying cgNA+ coarse-grain model. Parameter sets are provided to model dsDNA, including the possibility of epigenetically modified CpG dinucleotide steps, dsRNA, and DNA:RNA Hybrid double helical fragments. The cgNA+web interface is specifically designed to compare ground state shapes of different sequences of the same dsNA, or analogous sequences of different dsNAs. The cgNA+web server is freely available at cgDNAweb.epfl.ch without any login requirement.

Effect of high content nanohydroxyapatite composite scaffolds prepared via melt extrusion additive manufacturing on the osteogenic differentiation of human mesenchymal stromal cells.

The field of bone tissue engineering seeks to mimic the bone extracellular matrix composition, balancing the organic and inorganic components. In this regard, additive manufacturing (AM) of high content calcium phosphate (CaP)-polymer composites holds great promise towards the design of bioactive scaffolds. Yet, the biological performance of such scaffolds is still poorly characterized. In this study, melt extrusion AM (ME-AM) was used to fabricate poly(ethylene oxide terephthalate)/poly(butylene terephthalate) (PEOT/PBT)-nanohydroxyapatite (nHA) scaffolds with up to 45 wt% nHA, which presented significantly enhanced compressive mechanical properties, to evaluate their in vitro osteogenic potential as a function of nHA content. While osteogenic gene upregulation and matrix mineralization were observed on all scaffold types when cultured in osteogenic media, human mesenchymal stromal cells did not present an explicitly clear osteogenic phenotype, within the evaluated timeframe, in basic media cultures (i.e. without osteogenic factors). Yet, due to the adsorption of calcium and inorganic phosphate ions from cell culture media and simulated body fluid, the formation of a CaP layer was observed on PEOT/PBT-nHA 45 wt% scaffolds, which is hypothesized to account for their bone forming ability in the long term in vitro, and osteoconductivity in vivo.

Additive Manufactured Scaffolds for Bone Tissue Engineering: Physical Characterization of Thermoplastic Composites with Functional Fillers.

Thermoplastic polymer-filler composites are excellent materials for bone tissue engineering (TE) scaffolds, combining the functionality of fillers with suitable load-bearing ability, biodegradability, and additive manufacturing (AM) compatibility of the polymer. Two key determinants of their utility are their rheological behavior in the molten state, determining AM processability and their mechanical load-bearing properties. We report here the characterization of both these physical properties for four bone TE relevant composite formulations with poly(ethylene oxide terephthalate)/poly(butylene terephthalate (PEOT/PBT) as a base polymer, which is often used to fabricate TE scaffolds. The fillers used were reduced graphene oxide (rGO), hydroxyapatite (HA), gentamicin intercalated in zirconium phosphate (ZrP-GTM) and ciprofloxacin intercalated in MgAl layered double hydroxide (MgAl-CFX). The rheological assessment showed that generally the viscous behavior dominated the elastic behavior (G″ > G') for the studied composites, at empirically determined extrusion temperatures. Coupled rheological-thermal characterization of ZrP-GTM and HA composites showed that the fillers increased the solidification temperatures of the polymer melts during cooling. Both these findings have implications for the required extrusion temperatures and bonding between layers. Mechanical tests showed that the fillers generally not only made the polymer stiffer but more brittle in proportion to the filler fractions. Furthermore, the elastic moduli of scaffolds did not directly correlate with the corresponding bulk material properties, implying composite-specific AM processing effects on the mechanical properties. Finally, we show computational models to predict multimaterial scaffold elastic moduli using measured single material scaffold and bulk moduli. The reported characterizations are essential for assessing the AM processability and ultimately the suitability of the manufactured scaffolds for the envisioned bone regeneration application.

Effect of the reduced graphene oxide (rGO) compaction degree and concentration on rGO-polymer composite printability and cell interactions.

Graphene derivatives combined with polymers have attracted enormous attention for bone tissue engineering applications. Among others, reduced graphene oxide (rGO) is one of the preferred graphene-based fillers for the preparation of composites via melt compounding, and their further processing into 3D scaffolds, due to its established large-scale production method, thermal stability, and electrical conductivity. In this study, rGO (low bulk density 10 g L-1) was compacted by densification using a solvent (either acetone or water) prior to melt compounding, to simplify its handling and dosing into a twin-screw extrusion system. The effects of rGO bulk density (medium and high), densification solvent, and rGO concentration (3, 10 and 15% in weight) on rGO dispersion within the composite, electrical conductivity, printability and cell-material interactions were studied. High bulk density rGO (90 g L-1) occupied a low volume fraction within polymer composites, offering poor electrical properties but a reproducible printability up to 15 wt% rGO. On the other hand, the volume fraction within the composites of medium bulk density rGO (50 g L-1) was higher for a given concentration, enhancing rGO particle interactions and leading to enhanced electrical conductivity, but compromising the printability window. For a given bulk density (50 g L-1), rGO densified in water was more compacted and offered poorer dispersability within the polymer than rGO densified in acetone, and resulted in scaffolds with poor layer bonding or even lack of printability at high rGO percentages. A balance in printability and electrical properties was obtained for composites with medium bulk density achieved with rGO densified in acetone. Here, increasing rGO concentration led to more hydrophilic composites with a noticeable increase in protein adsorption. Moreover, scaffolds prepared with such composites presented antimicrobial properties even at low rGO contents (3 wt%). In addition, the viability and proliferation of human mesenchymal stromal cells (hMSCs) were maintained on scaffolds with up to 15% rGO and with enhanced osteogenic differentiation on 3% rGO scaffolds.

A dataset of high-resolution synchrotron x-ray photoelectron spectra of tarnished silver-copper surfaces before and after reduction with a remote helium plasma at atmospheric pressure.

The data presented in this article are related to the measurements in the contribution titled: 'Tarnished silver-copper surfaces reduction using remote helium plasma at atmospheric pressure studied by means of high-resolution synchrotron x-ray photoelectron microscopy' published in Corrosion Science. X-ray photoelectron spectra were collected from pure silver, sterling silver (92.5 w% Ag and 7.5 w% Cu) alloy and pure copper. These metals were artificially sulphidised. A remote helium plasma at atmospheric pressure was applied on the metallic and sulphidised state. Then the top layer of the 4 surface states were analysed at the NanoESCA beamline (Electron Spectroscopy for Chemical Analysis at the Nanoscale) at Elettra Sincrotrone Trieste. The instrument installed as an end station at the NanoESCA beamline of the Elettra storage ring combines an electrostatic Photo Electron Emission Microscope (PEEM) with a double-hemispherical ('IDEA') analyser, allowing the collection of photoemission electron microscopy (PEEM) images, X-ray photo electron-energy-filtered images and XPS spectra. The NanoESCA beamline provides electromagnetic radiation with variable polarization (linear, circular) and energies up to 1000 eV. Information for Cu3p, Cl2p, S2p, C1s and Ag3d were obtained by collecting spectra at 450 eV. The goal of the analyses was to determine how the plasma treatment changed the top layer of the metallic and sulphidised surface of pure silver, sterling silver and pure copper. This contribution focuses on the calibration of the collected XPS spectra, as well as the impact of the plasma treatment on the surface states.

A hybrid additive manufacturing platform to create bulk and surface composition gradients on scaffolds for tissue regeneration.

Scaffolds with gradients of physico-chemical properties and controlled 3D architectures are crucial for engineering complex tissues. These can be produced using multi-material additive manufacturing (AM) techniques. However, they typically only achieve discrete gradients using separate printheads to vary compositions. Achieving continuous composition gradients, to better mimic tissues, requires material dosing and mixing controls. No such AM solution exists for most biomaterials. Existing AM techniques also cannot selectively modify scaffold surfaces to locally stimulate cell adhesion. A hybrid AM solution to cover these needs is reported here. A dosing- and mixing-enabled, dual-material printhead and an atmospheric pressure plasma jet to selectively activate/coat scaffold filaments during manufacturing were combined on one platform. Continuous composition gradients in both 2D hydrogels and 3D thermoplastic scaffolds were fabricated. An improvement in mechanical properties of continuous gradients compared to discrete gradients in the 3D scaffolds, and the ability to selectively enhance cell adhesion were demonstrated.

Tuning Cell Behavior on 3D Scaffolds Fabricated by Atmospheric Plasma-Assisted Additive Manufacturing.

Three-dimensional (3D) scaffolds with optimum physicochemical properties are able to elicit specific cellular behaviors and guide tissue formation. However, cell-material interactions are limited in scaffolds fabricated by melt extrusion additive manufacturing (ME-AM) of synthetic polymers, and plasma treatment can be used to render the surface of the scaffolds more cell adhesive. In this study, a hybrid AM technology, which combines a ME-AM technique with an atmospheric pressure plasma jet, was employed to fabricate and plasma treat scaffolds in a single process. The organosilane monomer (3-aminopropyl)trimethoxysilane (APTMS) and a mixture of maleic anhydride and vinyltrimethoxysilane (MA-VTMOS) were used for the first time to plasma treat 3D scaffolds. APTMS treatment deposited plasma-polymerized films containing positively charged amine functional groups, while MA-VTMOS introduced negatively charged carboxyl groups on the 3D scaffolds' surface. Argon plasma activation was used as a control. All plasma treatments increased the surface wettability and protein adsorption to the surface of the scaffolds and improved cell distribution and proliferation. Notably, APTMS-treated scaffolds also allowed cell attachment by electrostatic interactions in the absence of serum. Interestingly, cell attachment and proliferation were not significantly affected by plasma treatment-induced aging. Also, while no significant differences were observed between plasma treatments in terms of gene expression, human mesenchymal stromal cells (hMSCs) could undergo osteogenic differentiation on aged scaffolds. This is probably because osteogenic differentiation is rather dependent on initial cell confluency and surface chemistry might play a secondary role.

3D additive manufactured composite scaffolds with antibiotic-loaded lamellar fillers for bone infection prevention and tissue regeneration.

Bone infections following open bone fracture or implant surgery remain a challenge in the orthopedics field. In order to avoid high doses of systemic drug administration, optimized local antibiotic release from scaffolds is required. 3D additive manufactured (AM) scaffolds made with biodegradable polymers are ideal to support bone healing in non-union scenarios and can be given antimicrobial properties by the incorporation of antibiotics. In this study, ciprofloxacin and gentamicin intercalated in the interlamellar spaces of magnesium aluminum layered double hydroxides (MgAl) and α-zirconium phosphates (ZrP), respectively, are dispersed within a thermoplastic polymer by melt compounding and subsequently processed via high temperature melt extrusion AM (~190 °C) into 3D scaffolds. The inorganic fillers enable a sustained antibiotics release through the polymer matrix, controlled by antibiotics counterions exchange or pH conditions. Importantly, both antibiotics retain their functionality after the manufacturing process at high temperatures, as verified by their activity against both Gram + and Gram - bacterial strains. Moreover, scaffolds loaded with filler-antibiotic do not impair human mesenchymal stromal cells osteogenic differentiation, allowing matrix mineralization and the expression of relevant osteogenic markers. Overall, these results suggest the possibility of fabricating dual functionality 3D scaffolds via high temperature melt extrusion for bone regeneration and infection prevention.

The role of histone tails in nucleosome stability: An electrostatic perspective.

We propose a methodology for the study of protein-DNA electrostatic interactions and apply it to clarify the effect of histone tails in nucleosomes. This method can be used to correlate electrostatic interactions to structural and functional features of protein-DNA systems, and can be combined with coarse-grained representations. In particular, we focus on the electrostatic field and resulting forces acting on the DNA. We investigate the electrostatic origins of effects such as different stages in DNA unwrapping, nucleosome destabilization upon histone tail truncation, and the role of specific arginines and lysines undergoing Post-Translational Modifications. We find that the positioning of the histone tails can oppose the attractive pull of the histone core, locally deform the DNA, and tune DNA unwrapping. Small conformational variations in the often overlooked H2A C-terminal tails had significant electrostatic repercussions near the DNA entry and exit sites. The H2A N-terminal tail exerts attractive electrostatic forces towards the histone core in positions where Polymerase II halts its progress. We validate our results with comparisons to previous experimental and computational observations.

The static and dynamic structural heterogeneities of B-DNA: extending Calladine-Dickerson rules.

We present a multi-laboratory effort to describe the structural and dynamical properties of duplex B-DNA under physiological conditions. By processing a large amount of atomistic molecular dynamics simulations, we determine the sequence-dependent structural properties of DNA as expressed in the equilibrium distribution of its stochastic dynamics. Our analysis includes a study of first and second moments of the equilibrium distribution, which can be accurately captured by a harmonic model, but with nonlocal sequence-dependence. We characterize the sequence-dependent choreography of backbone and base movements modulating the non-Gaussian or anharmonic effects manifested in the higher moments of the dynamics of the duplex when sampling the equilibrium distribution. Contrary to prior assumptions, such anharmonic deformations are not rare in DNA and can play a significant role in determining DNA conformation within complexes. Polymorphisms in helical geometries are particularly prevalent for certain tetranucleotide sequence contexts and are always coupled to a complex network of coordinated changes in the backbone. The analysis of our simulations, which contain instances of all tetranucleotide sequences, allow us to extend Calladine-Dickerson rules used for decades to interpret the average geometry of DNA, leading to a set of rules with quantitative predictive power that encompass nonlocal sequence-dependence and anharmonic fluctuations.

Nanoroughness, Surface Chemistry, and Drug Delivery Control by Atmospheric Plasma Jet on Implantable Devices.

Implantable devices need specific tailored surface morphologies and chemistries to interact with the living systems or to actively induce a biological response also by the release of drugs or proteins. These customized requirements foster technologies that can be implemented in additive manufacturing systems. Here, we present a novel approach based on spraying processes that allow to control separately topographic features in the submicron range (∼60 nm to 2 µm), ammine or carboxylic chemistry, and fluorophore release even on temperature-sensitive biodegradable polymers such as polycaprolactone (PCL). We developed a two-steps process with a first deposition of 220 nm silica and poly(lactic- co-glycolide) (PLGA) fluorescent nanoparticles by aerosol followed by the deposition of a fixing layer by an atmospheric pressure plasma jet (APPJ). The nanoparticles can be used to create the nanoroughness and to include active molecule release, while the capping layer ensures stability and the chemical functionalities. The process is enabled by a novel APPJ which allows deposition rates of 10-20 nm·s-1 at temperatures lower than 50 °C using argon as the process gas. This approach was assessed on titanium alloys for dental implants and on PCL films. The surfaces were characterized by Fourier transform infrared, atomic force microscopy, and scanning electron microscopy (SEM). Titanium alloys were tested with the preosteoblast murine cells line, while the PCL film was tested with fibroblasts. Cell behavior was evaluated by viability and adhesion assays, protein adsorption, cell proliferation, focal adhesion formation, and SEM. The release of a fluorophore molecule was assessed in the cell growing media, simulating a drug release. Osteoblast adhesion on the plasma-treated materials increased by 20% with respect to commercial titanium alloy implants. Fibroblast adhesion increased by a 100% compared to smooth PCL substrates. The release of the fluorophore by the dissolution of the PLGA nanoparticles was verified, and the integrity of the encapsulated drug model was confirmed.

Simultaneous microfabrication and tuning of the permselective properties in microporous polymers using X-ray lithography.

Microchannels are fabricated using a photosensitive polymer to which microporosity is tuned with different X-ray doses. Using hard X-ray irradiation, the micropattern is positioned with various geometries in a multi-level, three-dimensional structure, while controlling the pore size and transport properties of small molecules. This highly reliable fabrication process has potential for use in microfluidic devices with enhanced transport properties through microchannels.

Method for optimizing coating properties based on an evolutionary algorithm approach.

In industry as well as many areas of scientific research, data collected often contain a number of responses of interest for a chosen set of exploratory variables. Optimization of such multivariable multiresponse systems is a challenge well suited to genetic algorithms as global optimization tools. One such example is the optimization of coating surfaces with the required absolute and relative sensitivity for detecting analytes using devices such as sensor arrays. High-throughput synthesis and screening methods can be used to accelerate materials discovery and optimization; however, an important practical consideration for successful optimization of materials for arrays and other applications is the ability to generate adequate information from a minimum number of experiments. Here we present a case study to evaluate the efficiency of a novel evolutionary model-based multiresponse approach (EMMA) that enables the optimization of a coating while minimizing the number of experiments. EMMA plans the experiments and simultaneously models the material properties. We illustrate this novel procedure for materials optimization by testing the algorithm on a sol-gel synthetic route for production and optimization of a well studied amino-methyl-silane coating. The response variables of the coating have been optimized based on application criteria for micro- and macro-array surfaces. Spotting performance has been monitored using a fluorescent dye molecule for demonstration purposes and measured using a laser scanner. Optimization is achieved by exploring less than 2% of the possible experiments, resulting in identification of the most influential compositional variables. Use of EMMA to optimize control factors of a product or process is illustrated, and the proposed approach is shown to be a promising tool for simultaneously optimizing and modeling multivariable multiresponse systems.

A new method to position and functionalize metal-organic framework crystals.

With controlled nanometre-sized pores and surface areas of thousands of square metres per gram, metal-organic frameworks (MOFs) may have an integral role in future catalysis, filtration and sensing applications. In general, for MOF-based device fabrication, well-organized or patterned MOF growth is required, and thus conventional synthetic routes are not suitable. Moreover, to expand their applicability, the introduction of additional functionality into MOFs is desirable. Here, we explore the use of nanostructured poly-hydrate zinc phosphate (α-hopeite) microparticles as nucleation seeds for MOFs that simultaneously address all these issues. Affording spatial control of nucleation and significantly accelerating MOF growth, these α-hopeite microparticles are found to act as nucleation agents both in solution and on solid surfaces. In addition, the introduction of functional nanoparticles (metallic, semiconducting, polymeric) into these nucleating seeds translates directly to the fabrication of functional MOFs suitable for molecular size-selective applications.

Chemical tailoring of hybrid sol-gel thick coatings as hosting matrix for functional patterned microstructures.

A phenyl-based hybrid organic - inorganic coating has been synthesized and processed by hard X-ray lithography. The overall lithography process is performed in a two-step process only (X-rays exposure and chemical etching). The patterns present high aspect ratio, sharp edges, and high homogeneity. The coating has been doped with a variety of polycyclic aromatic hydrocarbon functional molecules, such as anthracene, pentacene, and fullerene. For the first time, hard X-rays have been combined with thick hybrid functional coatings, using the sol-gel thick film directly as resist. A new technique based on a new material combined with hard X-rays is now available to fabricate optical devices. The effect due to the high-energy photon exposure has been investigated using FT-IR and Raman spectroscopy, laser scanner, optical profilometer, and confocal and electron microscope. High-quality thick hybrid fullerene-doped microstructures have been fabricated.

Design, deposition, and characterization of multilayer coatings for the ultraviolet and visible-light coronagraphic imager.

The Ultraviolet and Visible-Light Coronagraphic Imager is the baseline coronagraph for the European Space Agency's payload Solar Orbiter, a solar mission whose launch in 2011 is expected. To prove the feasibility of its innovative design, a sounding rocket version of the same instrument has been approved by NASA. One of the main technological challenges of the instrument is the achievement of multilayer optical coatings with suitable properties. We describe the design, fabrication, and characterization of such coatings.

Study of the contaminant transport into granite microfractures using nuclear ion beam techniques.

Hydrated bentonite is a very plastic material and it is expected to enter in the rock microfractures at the granite/bentonite boundary of a deep geological high-level waste repository. This process is enhanced by the high swelling pressure of the clay. Since bentonite has a very good sorption capability for many radionuclides, the displacement of the clay might lead to a "clay-mediated" contaminant transport into the rock. The aim of this work is to study the contaminant transport into granite microfractures using nuclear ion beam techniques, and to determine to what extent the clay can favour it. To do so, bentonite previously doped with uranium, cesium and europium was put in contact with the surface of granite sheets. Granite sheets contacted with non-doped bentonite and with radionuclide solutions were also prepared as references. This allowed analysing the differences in the diffusion behaviour of the three systems: clay, radionuclides and clay plus radionuclides. A combination of Rutherford backscattering spectrometry (RBS) and other nuclear ion-beam techniques such as particle-induced X-ray emission (PIXE) and microPIXE was used to study the depth and lateral distribution of clay and contaminants inside granite. It was also tried to evaluate not only the diffusion depth and diffusion coefficients but also the different areas of the granite where the diffusants have a preferential access.